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- PDB-8t0v: Closed state of lysine 5,6-aminomutase from Thermoanaerobacter te... -

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Basic information

Entry
Database: PDB / ID: 8t0v
TitleClosed state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Components
  • D-lysine 5,6-aminomutase alpha subunit
  • D-lysine 5,6-aminomutase beta subunit
KeywordsISOMERASE / lysine 5 / 6-aminomutase / cobalamin / Vitamin B12 / Pyridoxal phosphate / radical
Function / homology
Function and homology information


cobalamin binding / catalytic activity / protein dimerization activity / metal ion binding
Similarity search - Function
D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily / D-Lysine 5,6-aminomutase alpha subunit superfamily / D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit / Dimerisation domain of d-ornithine 4,5-aminomutase / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / : / D-lysine 5,6-aminomutase beta subunit / D-lysine 5,6-aminomutase alpha subunit
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsTian, S. / Voss, P. / Pham, K. / Klose, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Catalysis in Motion: Large-Scale Domain Shift Enables Co-C Bond Homolysis in Lysine 5,6-Aminomutase
Authors: Tian, S. / Voss, P. / Pham, K. / Toba, D. / Liu, M. / Das, N. / Yachuw, S. / Denault, C. / Klose, T. / Uyeda, C.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: D-lysine 5,6-aminomutase beta subunit
C: D-lysine 5,6-aminomutase alpha subunit
D: D-lysine 5,6-aminomutase alpha subunit
A: D-lysine 5,6-aminomutase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8227
Polymers178,8474
Non-polymers1,9753
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein D-lysine 5,6-aminomutase beta subunit


Mass: 29728.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: TTE0727 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBT2
#2: Protein D-lysine 5,6-aminomutase alpha subunit


Mass: 59695.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: TTE0726 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBT3
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-X6I / S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine


Mass: 393.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N3O7PS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 55.2 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1060403 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211090
ELECTRON MICROSCOPYf_angle_d0.68415010
ELECTRON MICROSCOPYf_dihedral_angle_d7.5841541
ELECTRON MICROSCOPYf_chiral_restr0.0831698
ELECTRON MICROSCOPYf_plane_restr0.0041934

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